Rice Genetics IV - IRRI books - International Rice Research Institute

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Roschevicz RI. 1931. A contribution to the study of rice. Tr. Prikl. Bot. Genet. Sel. 27:3-133.Sampath S. 1962. The genus Oryza: its taxonomy and species interrelationships. Oryza 1:1-29.Sang T, Zhang DM. 1999. Reconstructing hybrid speciation using sequences of low copy nucleargenes: hybrid origins of five Paeonia species based on Adh gene phylogenies. Syst. Bot.24:148-163.Sarkar R, Raina SN. 1992. Assessment of genome relationships in the genus Oryza L. based onseed-protein profile analysis. Theor. Appl. Genet. 85:127-132.Sasaki T. 1998. The rice genome project in Japan. Proc. Natl. Acad. Sci. USA 95:2027-2028.Seberg O, Petersen G. 1998. A critical review of concepts and methods used in classical genomeanalysis. Bot. Rev. 64:372-417.Second G. 1982. Origin of the genic diversity of cultivated rice (Oryza spp.): study of thepolymorphism scored at 40 isozyme loci. Jpn. J. Genet. 57:25-57.Second G. 1985. A new insight into the genome differentiation in Oryza L. through isozymicstudies. In: Sharma AK, Sharma A, editors. Advances in chromosome and cell genetics.New Delhi (India): Oxford & IBH Publishing Co. p 45-78.Second G. 1991. Molecular markers in rice systematics and the evaluation of genetic resources.In: Bajaj YPS, editor. Biotechnology in agriculture and forestry. Berlin and Heidelberg(Germany): Springer-Verlag. p 468-494.Sharma SD. 1986. Evolutionary trends in genus Oryza. In: Rice genetics. Proceedings of theInternational Rice Genetics Symposium, 27-31 May 1985. Los Baños (Philippines): InternationalRice Research Institute. p 59-67.Sharma SD, Shastry SVS. 1965. Taxonomic studies in the genus Oryza. VI. A modified classificationof genus. Indian J. Genet. 25:173-178.Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF. 1998. The tortoise and the hare:choosing between non-coding plastome and nuclear Adh sequences for phylogeny reconstructionin a recently diverged plant group. Am. J. Bot. 85:1301-1315.Soltis PS, Soltis DE. 2000. The role of genetic and genomic attributes in the success of polyploids.Proc. Natl. Acad. Sci. USA 97:7051-7057.Stebbins GL. 1981. Coevolution of grasses and herbivores. Ann. Mo. Bot. Gard. 68:75-86.Swofford DL. 1991. When are phylogeny estimates from molecular and morphological dataincongruent? In: Miyamoto MM, Cracraft J, editors. Phylogenetic analysis of DNA sequences.New York (USA): Oxford University Press. p 295-333.Tanksley SD, McCouch SR. 1997. Seed banks and molecular maps: unlocking genetic potentialfrom the wild. Science 277:1063-1066.Tateoka T. 1962a. Taxonomic studies of Oryza. I. O. latifolia complex. Bot. Mag. Tokyo 75:418-427.Tateoka T. 1962b. Taxonomic studies of Oryza. II. Several species complexes. Bot. Mag.Tokyo 75:455-461.Tateoka T. 1963. Taxonomic studies of Oryza. III. Key to the species and their enumeration.Bot. Mag. Tokyo 76:165-173.Tateoka T. 1965a. Porteresia, a new genus of Gramineae. Bull. Natl. Sci. Mus. Tokyo 8:405-406.Tateoka T. 1965b. A taxonomy study of Oryza eichingeri and O. punctata. Bot. Mag. Tokyo78:156-163.Tateoka T, Pancho JV. 1963. A cytotaxonomic study of Oryza minuta and O. officinalis. Bot.Mag. Tokyo 76:366-373.Vaughan DA. 1989. The genus Oryza L.: current status of taxonomy. IRRI Research PaperSeries 138. Los Baños (Philippines): International Rice Research Institute.104 Song Ge et al
Vaughan DA. 1994. The wild relatives of rice: a genetic resources handbook. Los Baños (Philippines):International Rice Research Institute. 137 p.Wang ZY, Second G, Tanksley SD. 1992. Polymorphism and phylogenetic relationships amongspecies in the genus Oryza as determined by analysis of nuclear RFLPs. Theor. Appl. Genet.83:565-581.Wendel JF. 2000. Genome evolution in polyploids. Plant Mol. Biol. 42:225-249.Wendel JF, Albert VA. 1992. Phylogenetics of the cotton genus (Gossypium): character-stateweighted parsimony analysis of chloroplast-DNA restriction site data and its systematicand biogeographic implications. Syst. Bot. 17:115-143.Wendel JF, Doyle JJ. 1998. Phylogenetic incongruence: window into genome history and molecularevolution. In: Soltis DE, Soltis PS, Doyle JJ, editors. Molecular systematics ofplants II: DNA sequencing. Norwell, Mass. (USA): Kluwer Academic Publishers. p 265-296.Wolfe AD, Liston A. 1998. Contributions of PCR-based methods to plant systematics and evolutionarybiology. In: Soltis DE, Soltis PS, Doyle JJ, editors. Molecular systematics ofplants II: DNA sequencing. Norwell, Mass. (USA): Kluwer Academic Publishers. p 43-86.Xiao J, Grandillo S, Ahn SN, McCouch SR, Tanksley SD, Li J, Yuan L. 1996. Genes from wildrice improve yield. Nature 384:223-224.NotesAuthors' addresses: Song Ge, De-Yuan Hong, Laboratory of Systematic and EvolutionaryBotany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; TaoSang, Department of Botany and Plant Pathology, Michigan State University, East Lansing,MI 48824, USA; Bao-Rong Lu, Genetic Resources Center, International Rice ResearchInstitute, DAPO Box 7777, Metro Manila, Philippines.Acknowledgments: This work was supported by the Chinese Academy of Sciences (KZ951-B1-102), Michigan State University, and the Michigan Agricultural Experiment Station.Citation: Khush GS, Brar DS, Hardy B, editors. 2001. Rice genetics IV. Proceedings of theFourth International Rice Genetics Symposium, 22-27 October 2000, Los Baños, Philippines.New Delhi (India): Science Publishers, Inc., and Los Baños (Philippines): InternationalRice Research Institute. 488 p.Phylogeny of the genus Oryza . . . 105
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Retrotransposons of rice as a tool
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First, the Rice Genetics Cooperativ
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OverviewRice genetics from Mendel t
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Rice genetics from Mendelto functio
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nese cultivar Nipponbare. The chrom
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Gene symbolization in riceIn the ab
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Table 2. Some examples of mapping g
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and YAC libraries, respectively. Th
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gene from wild species is the intro
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ReferencesAbbasi FM, Brar DS, Carpe
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Nagao S. 1951. Genic analysis and l
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Yoshimura S, Yamanouchi U, Katayose
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important traits for which segregat
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trolled by a single recessive gene,
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AromaAromatic rice varieties often
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Submergence tolerance is an interes
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Kinoshita T, Maekawa M. 1986. Genet
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NotesAuthors’ addresses: J.N. Rut
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The Rockefeller Foundation has a lo
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Evolution and implementation of the
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Scientific progress and outputsIn t
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Another salient example is that of
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BOX NO. 1recent international works
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For the purposes of this discussion
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Because of the great diversity (sci
Page 66 and 67: eeders where final products to enha
Page 68 and 69: Chen S, Lin XH, Xu CG, Zhang Q. 200
Page 70 and 71: Toenniessen GH. 1998. Rice biotechn
Page 73 and 74: Molecular markers,genetic diversity
Page 75 and 76: Evolution and domestication of rice
Page 77 and 78: ABCDO. barthiiO. rufipogonO. longis
Page 79 and 80: Wild(O. rufipogon)Geographical diff
Page 81 and 82: South Asia (particularly on the wes
Page 83 and 84: al 1992, Sun et al 1996a,b,c), thou
Page 85 and 86: wild and cultivated types (Est10, W
Page 87 and 88: Cai HW, Morishima H. 2000a. Diversi
Page 89: Sato YI, Tang SX, Yang LU, Tang LH.
Page 92 and 93: The solid base laid by classical ri
Page 94 and 95: The synthesis shown in Figure 1 is
Page 96 and 97: Arabidopsis, long heralded as a “
Page 98 and 99: Monocots and eudicots: Is there sti
Page 100 and 101: Zhang H, Jia J, Gale MD, Devos KM.
Page 102 and 103: ility of rice productivity (Lu 1999
Page 104 and 105: Table 1 continuedIntrageneric class
Page 106 and 107: Molecular markers and evolutionary
Page 108 and 109: A100100521010078100991009894100O. s
Page 110 and 111: Two distinct types of sequences wer
Page 112 and 113: arthii and O. longistaminata, and t
Page 114 and 115: testing Ka/Ks between the homeologo
Page 119 and 120: Miniature inverted repeattransposab
Page 121 and 122: eau and Wessler 1992, 1994), rice (
Page 123 and 124: MITEs as a source of allelic divers
Page 125 and 126: ATIR Olo-D* Olo-CTIRBCas Exp Wan Sn
Page 127 and 128: Le QH, Wright S, Yu Z, Bureau T. 20
Page 129 and 130: Microsatellite markers in rice:abun
Page 131 and 132: make the best SSR markers for rice.
Page 133 and 134: Predicted frequency100,00080,000Cla
Page 135 and 136: Relationship between SSRs and genes
Page 139 and 140: are indicated with RM locus designa
Page 141 and 142: SSRs have been used to define intro
Page 143 and 144: provide a bridge for moving rapidly
Page 145 and 146: Ishii T, McCouch SR. 2000. Microsat
Page 147: NotesAuthors’ addresses: S.R. McC
Page 150 and 151: traits of economic importance (Mack
Page 152 and 153: Table 2. Tagging and mapping of som
Page 154 and 155: even at the juvenile stage. Several
Page 156 and 157: Chen et al (2000) transferred the b
Page 158 and 159: genome sequence of rice, this will
Page 160 and 161: Kurata N, Nagamura Y, Yamamoto K, H
Page 162 and 163: Witcombe JR, Hash CT. 2000. Resista
Page 165 and 166: QTL mapping in rice:a few critical
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M-QTLsM-QTLs are defined as single
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(genetic/statistical models and cor
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Table 5. The percentage of three ty
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Table 7. Some environment-specific
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ferently to the environments. Simil
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(case 3), one may infer that this g
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Simultaneous QTL introgression and
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Doebley J, Stec A, Gustus C. 1995.
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Visscher PM, Haley CS, Thompson R.
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unavailable until recently with the
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Table 1 continued.Trait QTL a Flank
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the remaining parts of the linkage
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Table 3. QTLs detected for yield an
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Table 6. Correlations of various pa
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The functions of these sequences ne
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Structural and functional genomicsT
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The International Rice GenomeSequen
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the RGP, a PAC (P1-derived artifici
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Progress of sequencing in the RGPWe
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ice genome sequencing to organize a
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Strategies and techniquesfor finish
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uses the quality values generated b
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with the advanced techniques requir
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times contain sufficient data to ma
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amplification of regions that previ
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4. Structure problems—subcloning
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estriction maps or optical maps are
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nal assembly may point to areas tha
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McMurray AA, Sulston JE, Quail MA.
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Sequence-tagged connector/DNA finge
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1999). The development of multiple-
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Transposable elements in the rice H
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ers, maps, mapping populations, and
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Miropeats-OSJNBa0065H03 1.2 cMThres
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NotesAuthors’ addresses: R.A. Win
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Sasaki 1997). Such analysis is ofte
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ABNipponbare × KasalathF 2QTL anal
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were classified into two groups bas
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effective at determining the genoty
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addition, some accessions of wild r
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Sasaki T, Burr T. 2000. Internation
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Mutational analysis has long been t
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marked by a deletion/chromosomal re
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analysis suggests that the mutation
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For drought-response screening, our
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Pi-7(t)Xa21Xa10Xa3Xa4Pi-1(t)Pi-k, P
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Although mutants with discrete gene
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Generation of T-DNA insertionaltagg
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Aprobe AEEprobe BpGA1633RBgus Tn p3
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Number of loci36%224%170%010 20 30F
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Table 2. GUS assay in roots of tran
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1999, Krysan et al 1999, Sato et al
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Transposons and functionalgenomics
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cesses. To study the interactions a
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Constructs were made with the aim o
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RBcis-effect of the adjacent strong
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Ac knockout mutagenesisThe Ac lines
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Table 2 summarizes the transformati
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ReferencesBaldwin D, Crane V, Rice
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NotesAuthors’ addresses: R. Greco
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These include T-DNA (Azpiroz-Leehan
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polyproteins and two identical 138-
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mutant. The mutation in the ent-kau
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primers (G1, G2) and two Tos17-spec
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of insertion mutants by sequencing
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Grandbastien M-A, Spielman A, Caboc
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NotesAuthors’ addresses: H. Hiroc
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human endeavor, greatly contributed
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Equally important as the genomic in
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Oryzabase is one of the most recent
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Database structureA characteristic
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types of users. An annotation datab
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ReferencesAntonio BA, Fang Z, Sanch
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Gene isolation and functionEnhancin
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Enhancing deployment of genes forbl
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mochi and Tsuyuake (Wu et al 1996).
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tive indica rice varieties supports
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transcription factor, resulting in
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facilitate breeding durable resista
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(Inukai et al 1994, Yu et al 1996,
Page 333 and 334:
Rossman AY, Howard RJ, Valent B. 19
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Molecular signaling in diseaseresis
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AOsRac1IED II III IV 214aaOsRac1 KC
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Japonica rice variety Kinmaze, whic
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Table 1. Characteristics of lesion-
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an effective inducer of host resist
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Takahashi A, Kawasaki T, Henmi K, S
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et al 2000). Sequence analysis of t
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612-amino acid protein, including t
Page 352 and 353:
Genetic dissection of the Xa21-medi
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ReferencesAnderson PA, Lawrence GJ,
Page 357 and 358:
Isolation of candidate genesfor tol
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Materials and methodsPlant material
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Microarray hybridization and data a
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Table 3. Most abundant transcripts
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Microarray technologyThe rapid accu
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view of procedures, pitfalls, and n
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Log(2) ratio1.51.0OC104E01—WCP1OC
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Table 5. Strongly regulated transcr
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ReferencesAdams MD, Soares MB, Kerl
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Acknowledgments: We thank Chris Bor
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y cells separating during tissue de
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(Erwee and Goodwin 1983). The sympl
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tion between the abundance of CDK t
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in a complex of 105 kDa. These resu
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Drew MC, Jackson MB, Giffard S. 197
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Umeda M, Umeda-Hara C, Yamaguchi M,
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asexual reproduction through apomix
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MPManual pollination by breeders×
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Search for apomixis in riceThere ar
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Issues related to achieving synthet
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come and may use imprinting to achi
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Embryo-inducing geneInactive ablati
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M 1 3 3 4 5 6 7 8 9 10 11 12 13 14
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embryos, several genes characterist
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Our search for a rice homologue of
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sequenced the two rice DMC1 genes a
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Gustine DL, Sherwood RT, Huff DR. 1
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Peel MD, Carman JG, Leblanc O. 1997
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TransformationEngineering for virus
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Engineering for virusresistance in
Page 419 and 420:
proteins, (2) the expression of dys
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Antisense and cosuppression RNA. Ex
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Table 1. Transgenic rice with patho
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the disease symptoms. Efforts from
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an ambisense coding strategy (Fig.
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first produced and shown to have vi
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McLean GD, Evans G. 1997. Some pote
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Waterhouse PM, Upadhyaya NM. 1998.
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duction in response to dehydration
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(KIKEKLPG) in the carboxyl terminus
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These three plasmids were used to t
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We now show the effects of the toba
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Since one major goal of plant scien
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Table 4. Copy number of transgenes
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Chan M-T, Chang H-H, Ho S-L, Tang W
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NotesAuthors’ address: Department
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initially fixed by phosphoenolpyruv
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High-level expression of maize C 4-
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The effect of illumination on PPDK
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ate in 2% O 2 can be limited by Pi
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Transgene integration,organization,
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duced by organogenesis, somatic emb
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ing transgene organization. FISH an
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ments and the integration of exogen
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Level 2: activation of local repair
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strongly suggested that plant facto
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other cases it was not. We observed
Page 475 and 476:
Gorbunova V, Levy AA. 1997. Non-hom
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Gene silencing and itsreactivation
Page 479 and 480:
Carbofuran (trade name, Furadan) is
Page 481 and 482:
Akb4xHpaIIJKA52 (R 0)52-6 (R 1)52-9
Page 483 and 484:
ABCDhptuidAmUbi1kb10.08.05.04.13.0F
Page 485 and 486:
Fig. 4. X-gluc staining of germinat
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eflect different causes for silenci
Page 489 and 490:
Table 4. Suppressors of silencing f
Page 491 and 492:
Garrick D, Fiering S, Martin DI, Wh
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Xu Y, Buchholz WG, DeRose RT, Hall
Page 496 and 497:
Rice molecular breeding workshopThi
Page 498 and 499:
the working group can develop a net
Page 500:
Rice genetics cooperativeA meeting
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